So, I've found a solution that worked for us. I found this KB article
(http://support.microsoft.com/kb/895855), which talks about
permissions issues resulting from an upgrade of exchange. Even though
we had not recently upgraded or even patched our Exchange server, we
had made a recent change to the log file settings. I have no idea if
the log change caused this problem, but went through and changed the
owner or the folders from myself (who sets up the folders and got put
in as the default owner) to a general admin account. This made the
folders visible once again.
Hope this helps others.